Five racemates (1-5) were isolated from Gentiana macrophylla, in which 2-5 were successfully separated into four pairs of enantiomers (2a and 2b, 3a and 3b, 4a and 4b, and 5a and 5b), whereas the resolution of 1 failed due to the hemiacetal functionality at the stereogenic center. Using electronic circular dichrosim calculation, the relationship of the molecular rotation direction and the carbon R/S chirality was revealed, and each pair of enantiomer was identified as (-)-(S)-gentianmacrol B (2a) and (+)-(R)-gentianmacrol B (2b), (-)-(S)-8-methoxy-gentianol (3a) and (+)-(R)-8-methoxy-gentianol (3b), (+)-(S)-8-methyl-gentianadine (4a) and (-)-(R)-8-methyl-gentianadine (4b), and (-)-(S)-gentianol (5a) and (+)-(R)-gentianol (5b). Besides, these compounds could be divided into two series, 1-2 containing the benzene ring moiety and 3-5 containing the pyridine ring moiety. Considering that their molecular skeleton could not be generated from the classical biosynthesis pathway in plants, the plausible biosynthesis pathways of 1-5 were deduced to be transformed from secoiridoids in G. macrophylla. Due to the significant difference in the pharmacological effect for the optical factor, our research provided new diverse molecules for further optical activity studies in drug research.